I just realized what im doing wrong.. If I swapped color values within palette then magenta would be black (if thats 1st color) and black would be magenta, so that affects the image and it becomes a mess.. like all my dark places using the black become magenta.

GIMP has the rearrange color map, where you drag the color you need first and it doesnt touch the image itself. Good I don't need extra tools or the ones you suggested but didnt know GIMP has that. Now I will only look if a script can do this as batch process,